TaqMan Human miRNA array profile of Mycobacterium tuberculosis H37Rv infected THP-1 differentiated macrophages cells.
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE94007 | GEO | 2017/04/20
SECONDARY ACCESSION(S): PRJNA363048
REPOSITORIES: GEO
Similar Datasets
Project description:To gain more insight in the biological expression and role of microRNAs in trophoblast cells, we then set up to determinate the miRNA expression pattern of four trophoblastic cell lines and compare them with the miRNA signature of isolated trophoblast Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 miRNAs. For each of two cards per sample (A and B), 9 ul of pre-amplified diluted sample was mixed with TaqMan reaction mix (Applied Biosystems) and loaded into miRNA TLDA cards (Applied Biosystems) by centrifugation. Cards were sealed, and qRT-PCR was performed with a real-time thermocycler (ABI-7900, Applied Biosystems) per manufacturer's recommendations.
2011-09-23 | GSE32346 | GEO
Project description:Expression profile of microRNA in lumbar spinal cord from MLC/SOD1G93A using Applied Biosystem Array Mouse MicroRNA A Card Lumbar Spinal Cord Ventral samples were collected from mice MLC/SOD1[G93A] and control FVB age matched at 4 month-old. Samples were collected for RNA extraction and analyzed on Taqman Array Mouse MicroRNA Card A version 3.0
2015-12-31 | E-GEOD-71193 | biostudies-arrayexpress
Project description:MicroRNA (667) profiling was done using TaqMan MicroRNA Arrays, which contains megaplex primer Pools covering Sanger miRBase version10 of Taqman Low Density Arrays (TLDA) platform across 50 samples along with the normals consisting of T cell lineage Acute Lymphoblastic Leukemia (T-ALL) and B cell lineage Acute Lymphoblastic Leukemia (B-ALL) subtypes which consists peripheral blood (PB) and bone marrow (BM) samples. The above isolated RNA which displayed good RIN value, linearity (R2>0.96), were used for reverse transcription (RT) reactions with the help of TaqMan MicroRNA Reverse Transcription Kit followed by PCR Reaction (ABI 7900 HT) as per illustration provided in kit. Real-time PCR was performed using an Applied Biosystems 7900 HT- TLDA Real-Time PCR System. A pre -amplification step of cDNA with pre-amp megaplex pool primers was done to significantly enhance the ability to detect highly down regulated miRNAs. The TaqMan human microRNA arrays consists of two plates, pool A and pool B. RNU 46 and RNU 48 were used as endogenous controls for data normalization. Another control not related to human is also included as a negative control. Each TaqMan Assay was run in quadruplicate. RNU 46 and RNU 48 expression was consistent in all the samples and displayed good range of CTs values 22–24 ) where as in ‘No Template’ Control (NTC) CT value was above 38. The average CT values of total profiled miRNAs in all samples were normalized with RNU 46 & RNU 48 using spotfire (statminer) software and fold change were represented in terms of log 10, 2 - Δ Δ CT (RQ ) and log10RQ. Only valid and significant miRNAs were picked up for further analysis.
2014-08-14 | GSE60386 | GEO
Project description:Aim of this study was to identify miRNAs which are regulated by LIF in different trophoblastic cell lines Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TaqMan Arrays. Quantitative real-time PCR was performed for 768 miRNAs. For each of two cards per sample (A and B), 9 ul of pre-amplified diluted sample was mixed with TaqMan reaction mix (Applied Biosystems) and loaded into miRNA TLDA cards (Applied Biosystems) by centrifugation. Cards were sealed, and qRT-PCR was performed with a real-time thermocycler (ABI-7900, Applied Biosystems) per manufacturer's recommendations.
2019-09-01 | GSE130489 | GEO
Project description:We aimed to identify urinary exosomal miRNAs associated with PCa metastasis and develop a non-invasive risk-scoring model for PCa metastasis in this study. MiRNA profiles were examined using the Taqman low-density miRNA array (TLDA). Megaplex reverse transcription reactions and pre-amplification reactions were performed to increase the quantity of cDNA for miRNA expression analysis using the Megaplex PreAmp Primers Human Pool A and TaqMan PreAmp Master Mix (Thermo Fisher Scientific). MiRNA expression was evaluated via the TLDA panel A v2.0 (Thermo Fisher Scientific). Raw data were processed using the QuantStudio Real-Time PCR Software (Thermo Fisher Scientific) to determine a cycle threshold (Ct) value for each miRNA.
2021-06-07 | GSE173094 | GEO
Project description:To gain more insight in the expression and role of microRNAs in trophoblastic cells, we have assessed the miRNA expression pattern of four trophoblastic cell lines and have compared them with the miRNA signature of human isolated 3rd trimester cytotrophoblast cells. Total RNA was reverse-transcribed, pre-amplified with miRNA-specific primers, and loaded into TLDA cards. Quantitative real-time PCR was performed for 768 miRNAs. For each of two cards per sample (A and B), 9 ul of pre-amplified diluted sample was mixed with TaqMan reaction mix (Applied Biosystems) and loaded into miRNA TLDA cards (Applied Biosystems) by centrifugation. Cards were sealed, and qRT-PCR was performed at a real-time thermocycler (ABI-7900, Applied Biosystems) following the manufacturer's recommendations. MiRNA signatures of human primary 3rd trimester trophoblast cells were compared with those of four trophoblastic cell lines
2011-09-22 | E-GEOD-32346 | biostudies-arrayexpress
Project description:We determined expression profiles of 667 miRNAs using TaqMan Low Density Arrays (TLDA-TaqMan Array Human MicroRNA Card Set v2.0, Applied Biosystems) in 8 samples of colorectal cancer tissues and 8 samples of paired non-tumoral colonic tissues.
2012-03-31 | E-MEXP-3515 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are non-coding RNAs that play a fundamental role in regulation of gene expression affecting differentiation and development. In particular, miRNAs have been described to regulate genes important for pancreatic development and islet function. The aim of this work was to determine the miRNA expression signature in human pancreatic alpha and beta cells. miRNA stability to fixation allowed the study of microRNA in pure populations of human alpha and beta cells sorted by FACS after intracellular staining with glucagon and insulin, respectively. The determination of the specific group of miRNAs expressed in the human pancreatic alpha and beta cells may further the understanding of gene expression regulation of the islet differentiation process. The alpha and beta cells come from 6 different preparations of human pancreatic islets from donors. In this study we define expression profiles of a total of 665 miRNAs for pancreatic alpha and beta cells. For this purpose, cells were fixed with paraformaldehyde, 7AAD was applied to exclude dead cells. Then, cells were sorted after intracellular staining with C peptide to detect beta cells and glucagon to detect alpha cells. After sorting, we confirmed enriched beta cells have a purity of on average over 98%. Enriched alpha cells have a purity of on average over 98%. To determine the miRNA expression profiles, we used human miRNA TLDAs version 2. For each sample card A and card B were run after cDNA synthesis and 12 cycles of preamplification according to the manufacturer protocol. Each TLDA card A contains 1 probe for the endogenous control RNU48 while each TLDA card B contains 4 replicates of the RNU48 probe. Analysis of these controls allows calculating the intra- and inter-assay variation. Quantitative values (RQ) were calculated measuring the ddCt between the Ct values of each miRNA and the Ct value of the small nucleolar RNU48 RNA comparing the target sample and the control sample.
2013-01-30 | E-GEOD-38360 | biostudies-arrayexpress
Project description:Breast cancer is a common disease with distinct tumor subtypes which can be phenotypically characterized by estrogen receptor, progesterone receptor and HER2/neu receptor status. MiRNAs play regulatory roles in tumor initiation and progression. Altered miRNA expression has been demonstrated in a variety of cancer states to date presenting the potential for exploitation as cancer specific biomarkers. Blood presents an attractive medium biomarker discovery. This study investigated systemic miRNAs differentially expressed in Luminal A (ER+PR+HER2/neu-) breast cancer and their effectiveness as oncologic biomarkers in the clinical setting. Blood samples were prospectively collected from consenting patients with Luminal A breast cancer (n=10) and controls (n=10). RNA was extracted, reverse transcribed and subjected to microarray analysis (n=10 Luminal A; n=10 Control). Differentially expressed miRNAs were identified by artificial neural network (ANN) data-mining algorithms. Ethical approval was granted by the Clinical Research Ethics Committee, Galway Roscommon University Hospital Group. Written informed consent was obtained from all study participants. Blood samples were prospectively collected from 20 women; this included 10 consecutive women with a new diagnosis of Luminal A breast cancer and 10 healthy control participants. Luminal A status was confirmed with immunohistochemistry and fluorescence in situ hybridization (FISH). The blood samples for the healthy control group were collected from women residing in the same catchment area as the cancer cases. These women had no personal history of malignancy and no current inflammatory or infectious condition. Venous non-fasting whole blood samples were collected in BD vacutainers M-BM-. containing 18mg dipotassium EDTA anticoagulant (BD-Plymouth, PL6 7BP, UK). Total RNA was extracted from blood (1ml) using TRI Reagent BD (Molecular Research Centre, Inc). RNA concentration and integrity were evaluated by NanoDrop spectrophotometry (NanoDrop ND-1000 Technologies Inc., DE, USA) and Agilent Bioanalyzer RNA 6000 NanoChip Kit Series II (Agilent Technologies, Germany) analysis, respectively. MiRNA microarray profiling Expression profiling of circulating miRNAs was performed using TaqMan miRNA arrays and assays in accordance with the manufacturerM-bM-^@M-^Ys instructions (Taqman Low Density Array Human microRNA Card A and Card B, Applied Biosystems, Foster City, CA, USA). In short, total RNA was reverse transcribed using Megaplex primer pool A (Applied Biosystems) which contained sequence-specific primers for 381 specific miRNAs plus 3 controls (pool A). An additional panel of 384 miRNAs (381 miRNAs and 3 controls, pool B) was performed on a subset of 4 cancers and 4 controls. Real-time quantitative PCR was performed for 667 miRNAs, using A and B microfluidic cards, each containing primers and probes for 381 specific miRNAs plus 3 controls and thermal-cycled on an Applied Biosystems 7900HT instrument. The TLDA cards contain three endogenous controls (RNU44, RNU48 and MammU6 which is repeated four times on each card). Each card also contains a negative control, an assay unrelated to any human species, ath-miR-159a.
2013-04-24 | E-GEOD-46355 | biostudies-arrayexpress
Project description:In the effort to identify novel, relevant prognostic factors for the clinical monitoring of patients affected by squamous cell carcinomas of the oral cavity (SCCOC) we have pursued a molecular screening at the gene and protein level on 166 surgical specimens derived from patients with an accessible clinical history and >2 years follow-up. The screening was focalized on cell surface proteoglycans (PGs) based upon the assumption that altered expression of individual or groups of PGs may predict disease course and therapeutic response, and thereby allow for a clusterization of patients in discrete subsets. The 11 PGs contemplated in the screening and including syndecan-1-4 (SDC1-SDC4), glypican-1-6 (GPC1-GPC6) and NG2, were found to be transcribed at variable levels and with a decreasing frequencies SDC1>SDC4>SDC2>SDC3>GPC4>GPC3>GPC1 >GPC5>CSPG4>GPC6>GPC2. SCCOC cells de novo transcribed GPC2, GPC5 and NG2 and regulated all SDCs, GPC1, -3, -4 and -6, suggesting that an altered surface profile of PG is a characterizing trait of these tumor cells In situ distributional analysis of these PGs on a total of 149 cases revealed many fewer lesions actually translated the molecules which were detected with a frequency range of 14% (SDC2) to 92% (SDC1). Noteworthy was, however, that SDC2 was present in the intra-lesional stroma and in association with neovessels in all the cases, suggesting that this specific PG was a key element of stromal fibroblasts and angiogenic structures. Poor translational efficacy of several of the PGs was accompanied by an apparent retention of the molecules within the cytoplasm of SCCOC cells. This finding suggest that modulated expression of cell surface PGs may be a representative secondary event in SCCOC and that these carcinoma cells do not mount up an effective intracellular machinery for proper shuttling and membrane incorporation of the PGs. A total of 166 surgical specimens of primary SCCOC were collected after informed consent from individuals who underwent surgical removal of the tumor lesions and RNA from 119 surgical specimens were extracted; a pool of RNAs extracted from 5 normal epithelia tissues was adopted as a sample calibrator (HEALTHY sample). cDNA from each samples and from pool of normal epithelial were loaded on TLDA and amplified. HEALTHY sample were amplified 20 times in two replicates (in each TLDA card); each patient sample were amplified 1 time in two replicates and 7 samples of them were loaded two times in a separate TLDA card (for a total of 4 replicates).
2013-11-01 | E-GEOD-33788 | biostudies-arrayexpress